Once a Next Action has been determined as a part of a Project, do you dissect the Project and come up with Multiple Next Actions, and return (organize) them to the Next Action Notebooks? or leave them in the Project's Notebook
None of the above. I don't create a separate notebook for each project because Evernote limits you to something like 250 notebooks (unless something has changed recently that I'm not aware of). Instead, I have one notebook for all of my projects and each project is a note within that notebook.
I also have a separate notebook for each context (calls, errands, home, computer, etc.) where I store all of the appropriate next action items.
If I have a particular project that requires support material beyond what I can comfortably input in or attach to a single note, I'll create a notebook for that project. The vast majority of mine don't require it, though.
If you really feel a need to create a "link" between projects and actions, you can create a keyword or words that you input in the body of each action. You can then find those actions using Evernote's robust and easy-to-use search feature. You can also use tags. I rarely do either, though, as I've learned for the most part to do without such linkages. I wouldn't suggest trying to use these workarounds for all of your projects as doing so would likely get unwieldy.